A linear-time algorithm for finding the longest segment which scores above a given threshold

Abstract

This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in which the average of the scores is above a fixed threshold. The problem originates from molecular sequence analysis: for instance, the algorithm can be employed to identify long GC-rich regions in DNA sequences. The algorithm can also be used to trim low-quality ends of shotgun sequences in a preprocessing step of whole-genome assembly.